Variant report

Variant	rs11615783
Chromosome Location	chr12:57622492-57622493
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:57622485-57625200	PFSK-1	brain:	n/a	n/a
2	HCFC1	chr12:57622313-57625003	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:57480170..57482164-chr12:57622267..57624511,2	MCF-7	breast:
2	chr12:54673520..54675389-chr12:57621461..57623953,2	MCF-7	breast:
3	chr12:57622307..57625065-chr12:57914079..57916302,2	K562	blood:

Variant related genes	Relation type
SHMT2	TF binding region
ENSG00000166881	Chromatin interaction
ENSG00000175197	Chromatin interaction
ENSG00000166987	Chromatin interaction
ENSG00000135486	Chromatin interaction
ENSG00000094916	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs11172124	0.84[EUR][1000 genomes]
rs11612551	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61736007	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73120022	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7485577	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1040850	chr12:57055011-57679209	Strong transcription Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	181 gene(s)	inside rSNPs	diseases
2	nsv518980	chr12:57532982-57637593	Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	esv1810281	chr12:57558657-57641094	Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Weak transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
4	esv1827238	chr12:57561918-57641094	Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
5	esv1796377	chr12:57577246-57638936	Bivalent/Poised TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
6	esv1809338	chr12:57580227-57628338	Flanking Bivalent TSS/Enh Strong transcription Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
7	esv1827692	chr12:57582852-57651345	Bivalent Enhancer Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
8	nsv519293	chr12:57583672-57637593	Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
9	nsv899116	chr12:57597169-57623363	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:57611400-57623000	Weak transcription	Right Atrium	heart
2	chr12:57615000-57622800	Weak transcription	A549	lung
3	chr12:57619800-57623000	Weak transcription	Gastric	stomach
4	chr12:57620400-57622800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
5	chr12:57620600-57623400	Weak transcription	Pancreas	Pancrea
6	chr12:57621000-57623000	Weak transcription	Right Ventricle	heart
7	chr12:57621200-57622600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr12:57621200-57622600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr12:57621200-57622600	Weak transcription	HSMM	muscle
10	chr12:57621200-57623000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
11	chr12:57621200-57623000	Enhancers	Primary T helper cells fromperipheralblood	blood
12	chr12:57621400-57622800	Weak transcription	HMEC	breast
13	chr12:57621600-57622600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr12:57621600-57622800	Weak transcription	Colonic Mucosa	Colon
15	chr12:57621600-57622800	Weak transcription	Placenta	Placenta
16	chr12:57621600-57623200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
17	chr12:57621600-57623200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr12:57621800-57622600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr12:57621800-57622600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr12:57621800-57622800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr12:57621800-57622800	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr12:57621800-57622800	Weak transcription	NHLF	lung
23	chr12:57621800-57623000	Enhancers	Primary hematopoietic stem cells	blood
24	chr12:57621800-57623000	Enhancers	Primary hematopoietic stem cells short term culture	blood
25	chr12:57621800-57623000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
26	chr12:57621800-57623000	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr12:57621800-57623400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr12:57622200-57622600	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr12:57622400-57622600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr12:57622400-57622600	Enhancers	Primary T killer memory cells from peripheral blood	blood
31	chr12:57622400-57622600	Enhancers	Dnd41	blood
32	chr12:57622400-57622800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr12:57622400-57622800	Enhancers	Primary T helper cells PMA-I stimulated	--
34	chr12:57622400-57622800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
35	chr12:57622400-57622800	Enhancers	GM12878-XiMat	blood
36	chr12:57622400-57622800	Enhancers	K562	blood
37	chr12:57622400-57622800	Enhancers	Osteobl	bone
38	chr12:57622400-57623000	Enhancers	Breast Myoepithelial Primary Cells	Breast
39	chr12:57622400-57623000	Enhancers	Primary B cells from cord blood	blood
40	chr12:57622400-57623000	Enhancers	Primary T cells fromperipheralblood	blood
41	chr12:57622400-57623000	Enhancers	Primary T helper naive cells from peripheral blood	blood
42	chr12:57622400-57623000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
43	chr12:57622400-57623000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr12:57622400-57623000	Enhancers	NHDF-Ad	bronchial
45	chr12:57622400-57623200	Enhancers	Primary B cells from peripheral blood	blood

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